| 1. |
- Claussnitzer, Melina, et al.
(författare)
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Leveraging cross-species transcription factor binding site patterns: from diabetes risk Loci to disease mechanisms.
- 2014
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Ingår i: Cell. - : Elsevier BV. - 1097-4172 .- 0092-8674. ; 156:1-2, s. 343-358
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central to disease susceptibility. We show that integrative computational analysis of phylogenetic conservation with a complexity assessment of co-occurring transcription factor binding sites (TFBS) can identify cis-regulatory variants and elucidate their mechanistic role in disease. Analysis of established type 2 diabetes risk loci revealed a striking clustering of distinct homeobox TFBS. We identified the PRRX1 homeobox factor as a repressor of PPARG2 expression in adipose cells and demonstrate its adverse effect on lipid metabolism and systemic insulin sensitivity, dependent on the rs4684847 risk allele that triggers PRRX1 binding. Thus, cross-species conservation analysis at the level of co-occurring TFBS provides a valuable contribution to the translation of genetic association signals to disease-related molecular mechanisms.
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| 2. |
- Oskolkov, Nikolay, et al.
(författare)
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Nematic Ordering of Polymers in Confined Geometry Applied to DNA Packaging in Viral Capsids.
- 2011
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 115:3, s. 422-432
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Tidskriftsartikel (refereegranskat)abstract
- A density functional theory of the spatial distribution and biaxial nematic order of polymers of arbitrary length and rigidity inside a spherical cavity is proposed. The local order of different chain segments is considered as an alignment to a spatially varying director field of cylindrical symmetry. The steric interactions are taken into account in the second virial approximation. Polymer density and orientational order distributions inside the spherically cavity are the principal results. It was found that short and flexible polymers were located at the center of the sphere and were orientationaly disordered. Upon increasing polymer length and/or polymer rigidity, the location of the polymer was continuously shifted toward the surface of the spherical cavity and the polymer segments became gradually more aligned. Parameters have been selected to model the behavior of genomes in spherical viral capsids.
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| 3. |
- Vikman, Petter, et al.
(författare)
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RNA sequencing: current and prospective uses in metabolic research.
- 2014
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Ingår i: Journal of Molecular Endocrinology. - 1479-6813. ; 53:2, s. 93-101
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Forskningsöversikt (refereegranskat)abstract
- Previous global RNA analysis was restricted to known transcripts in species with a defined transcriptome. Next generation sequencing has transformed transcriptomics by making it possible to analyse expressed genes with an exon level resolution from any tissue in any species without any a priori knowledge of which genes that are being expressed, splice patterns or their nucleotide sequence. In addition, RNA sequencing is a more sensitive technique compared with microarrays with a larger dynamic range, and it also allows for investigation of imprinting and allele-specific expression. This can be done for a cost that is able to compete with that of a microarray, making RNA sequencing a technique available to most researchers. Therefore RNA sequencing has recently become the state of the art with regards to large-scale RNA investigations and has to a large extent replaced microarrays. The only drawback is the large data amounts produced, which together with the complexity of the data can make a researcher spend far more time on analysis than performing the actual experiment.
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| 4. |
- Zhou, Yuedan, et al.
(författare)
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TCF7L2 is a master regulator of insulin production and processing
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6419-6431
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies have revealed > 60 loci associated with type 2 diabetes ( T2D), but the underlying causal variants and functional mechanisms remain largely elusive. Although variants in TCF7L2 confer the strongest risk of T2D among common variants by presumed effects on islet function, the molecular mechanisms are not yet well understood. Using RNA-sequencing, we have identified a TCF7L2-regulated transcriptional network responsible for its effect on insulin secretion in rodent and human pancreatic islets. ISL1 is a primary target of TCF7L2 and regulates proinsulin production and processing via MAFA, PDX1, NKX6.1, PCSK1, PCSK2 and SLC30A8, thereby providing evidence for a coordinated regulation of insulin production and processing. The risk T-allele of rs7903146 was associated with increased TCF7L2 expression, and decreased insulin content and secretion. Using gene expression profiles of 66 human pancreatic islets donors', we also show that the identified TCF7L2-ISL1 transcriptional network is regulated in a genotype-dependent manner. Taken together, these results demonstrate that not only synthesis of proinsulin is regulated by TCF7L2 but also processing and possibly clearance of proinsulin and insulin. These multiple targets in key pathways may explain why TCF7L2 has emerged as the gene showing one of the strongest associations with T2D.
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